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- PDB-8dpk: structure of T. brucei RESC5 -

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Basic information

Entry
Database: PDB / ID: 8dpk
Titlestructure of T. brucei RESC5
ComponentsRESC5
KeywordsPROTEIN BINDING / RESC5 / RESC6 / RNA editing substrate binding complex / kRNA editing / platform / gRNA
Function / homologyL-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsSchumacher, M.A. / Salinas, R. / Cannistraci, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Plos One / Year: 2023
Title: Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5.
Authors: Salinas, R. / Cannistraci, E. / Schumacher, M.A.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RESC5
D: RESC5


Theoretical massNumber of molelcules
Total (without water)66,8662
Polymers66,8662
Non-polymers00
Water5,495305
1
A: RESC5


Theoretical massNumber of molelcules
Total (without water)33,4331
Polymers33,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RESC5


Theoretical massNumber of molelcules
Total (without water)33,4331
Polymers33,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.606, 80.441, 76.076
Angle α, β, γ (deg.)90.000, 102.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RESC5


Mass: 33432.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 60% Tascimate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→54.54 Å / Num. obs: 38130 / % possible obs: 99.1 % / Redundancy: 3 % / CC1/2: 0.994 / Rpim(I) all: 0.044 / Rsym value: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 1.94→2.01 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2269 / CC1/2: 0.673 / Rpim(I) all: 0.228 / Rsym value: 0.274

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→54.54 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1620 4.25 %
Rwork0.221 36510 -
obs0.2226 38130 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.57 Å2 / Biso mean: 29.2768 Å2 / Biso min: 8.92 Å2
Refinement stepCycle: final / Resolution: 1.94→54.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 0 305 4577
Biso mean---29.56 -
Num. residues----549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-20.3741140.33052269238373
2-2.060.33061170.29732826294389
2.06-2.140.31141430.2733114325799
2.14-2.220.29421380.257931263264100
2.22-2.320.30541380.24483140327899
2.32-2.440.28961320.24663137326999
2.44-2.60.26631420.23923113325599
2.6-2.80.31431300.24493156328699
2.8-3.080.26961480.22573133328199
3.08-3.520.25411330.21043137327099
3.53-4.440.18681460.17033151329799
4.44-54.540.22161390.18593208334799

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